Enteroviruses are responsible for large numbers of infections. There may be between 30 million to 50 million illnesses that are ascribable to enteroviruses each year in the United States (Center for Disease Control and Prevention, MMWR 46:748-750, 1997-1999; Strikas et al., J. Infect. Dis. 146:346-351, 1986; Rotbart in Human Enterovirus Infections, H. A. Rotbart (ed.) ASM Press, Washington, D.C., pp. 401-418, 1995). Enterovirus infections lead to 30,000 to 50,000 hospitalizations each year for aseptic meningitis, myocarditis, encephalitis, acute hemorrhagic conjunctivitis, nonspecific febrile illnesses, and upper respiratory infections (Melnick, Biologicals 21:305-309, 1993; Morens et al., in Human Enterovirus Infections, H. A. Rotbart (ed.) ASM Press, Washington, D.C., pp. 3-23, 1995; Melnick in Fields Virology (B. N. Fields et al. (eds.)) 3rd ed., Lippincott-Raven Publishers, Philadelphia, pp. 655-712, 1996). Enteroviruses are also implicated in acute flaccid paralysis in animal models, as well as in dilated cardiomyopathy and have been linked to chronic fatigue syndrome (Clements et al., J. Med. Virol. 45:156-161, 1995).
One of the issues in both diagnostic and epidemiological studies of enterovirus (EV)(which includes the extremely common rhinovirus (RV)) infections in children and adults is that these viruses share an extremely high degree of sequence similarity. Quantitative PCR (qPCR) for RV and other EV viruses often results in cross-priming that can lead to misidentification of the virus present in clinical material and connection of disease states to the wrong species of virus. Further, it is almost impossible to successfully identify individuals that are suffering from co-infections of RV and another EV by standard qPCR methods.
Thus, there remains a need for compositions and methods for identifying, subtyping, and/or classifying viral infections like enterovirus infections in medium to high throughput, cost effective fashion.